There are data and labeling errors in
RT-PCR results reflecting transcript abundance are shown for rice genes identified by GeneChip expression analysis as the ten (or fewer) most significantly differentially expressed in response to (A)
Please see the corrected
There is an error in Figure 2, Table S1, Table S6, and Table S9. Release 7.0 Locus ID
There is an additional error in Figure 2 and Table S1, that is also in Table S4. In Figure 2, Table S1, and Table S4, the Release 7.0 Locus ID recorded for data associated with probeset Os.46631.1.S1_x_at is
There is additional information to add to Table S9. Primers used to amplify
There are two errors in
TAL effector | Target Locus ID |
Probe set ID(s) | Fold change 2-96h Xoc |
Fold change Mock-Xoc 96h |
EBE Score |
EBE rel. score |
EBE rank |
EBE to TLS |
EBE to TXS |
EBE to TATA box |
EBE to Y patch |
Induced by | Description | ||
Xag expressing the |
|||||||||||||||
Tal4a | 01g27210 | Os.7911.1.S1_at | 1.63 | 1.66 | 1.8E-01 | 29.22 | 2.85 | 341 | 253 | 143 | -50 | none | + | - | Glutathione S-transferase, putative, expressed |
Tal6 | 01g31220 | Os.6438.1.S1_a_at Os.6438.2.S1_x_at | 1.48 1.48 | 1.53 1.52 | 8.0E-02 1.1E-02 | 18.75 | 2.38 | 685 | 157 | 152 | none | 33 | - | + | Expressed protein |
Tal2d | 01g51040 | Os.53457.1.S1_at | 2.30 | 2.23 | 1.9E-01 | 14.32 | 2.19 | 324 | 527 | none | -328 | 0 | + | - | Transmembrane protein 16K, putative, expressed |
Tal9b | 01g51040 | Os.53457.1.S1_at | 2.30 | 2.23 | 1.9E-01 | 14.07 | 2.81 | 275 | 18 | 0 | -299 | none | - | + | Transmembrane protein 16K, putative, expressed |
Tal2g | 01g52130 | Os.41841.1.S1_at | 13.00 | 9.59 | 1.3E-06 | 13.94 | 1.97 | 77 | 427 | 58 | 28 | none | - | + | Sulfate transporter, putative, expressed |
Tal3b | 01g53220 | Os.35681.1.S1_at | 3.50 | 4.12 | 2.2E-06 | 17.72 | 2.92 | 611 | 146 | -5 | -137 | none | nd | nd | HSF-type DNA-binding domain containing protein, expressed |
Tal6 | 02g14770 | Os.2450.1.S1_a_at Os.2450.3.S1_x_at | 1.88 1.85 | 1.77 1.55 | 1.3E-02 6.8E-02 | 18.48 | 2.35 | 569 | 92 | 48 | -70 | -37 | + | - | Phosphoenolpyruvate carboxylase, putative, expressed |
Tal11a | 02g15290 | Os.56119.1.S1_at | 1.72 | 4.93 | 4.1E-07 | 20.15 | 3.18 | 582 | 422 | none | -288 | none | + | - | VQ domain containing protein, putative, expressed |
Tal5a | 02g15290 | Os.56119.1.S1_at | 1.72 | 4.93 | 4.1E-07 | 23.32 | 1.88 | 107 | 148 | 30 | -3 | -180 | - | + | VQ domain containing protein, putative, expressed |
Tal7 | 02g15710 | OsAffx.2629.1.S1_at | 5.70 | 5.52 | 8.4E-02 | 15.75 | 1.94 | 265 | 951 | none | 150 | 434 | nd | nd | Plastocyanin-like domain containing protein, putative, expressed |
Tal3b | 02g34970 | Os.47735.1.S1_at | 9.07 | 5.31 | 4.0E-07 | 15.33 | 2.53 | 75 | 110 | 29 | -282 | none | - | + | No apical meristem protein, putative, expressed |
Tal2a | 02g43760 | Os.1349.1.S1_at OsAffx.2950.1.S1_s_at | 1.25 1.23 | 1.45 1.32 | 1.7E-03 5.3E-03 | 15.87 | 1.75 | 21 | 521 | none | -334 | -5 | nd | + | Ubiquitin carboxyl-terminal hydrolase, family 1, putative, expressed |
Tal7 | 02g43760 | Os.1349.1.S1_at OsAffx.2950.1.S1_s_at | 1.25 1.23 | 1.45 1.32 | 1.7E-03 5.3E-03 | 16.45 | 2.03 | 547 | 628 | 341 | 17 | 117 | + | - | Ubiquitin carboxyl-terminal hydrolase, family 1, putative, expressed |
Tal3c | 02g47660 | Os.7751.1.S1_at | 2.25 | 2.24 | 1.9E-03 | 10.93 | 1.92 | 53 | 140 | -63 | -98 | none | - | + | Basic helix-loop-helix, putative, expressed |
Tal4c | 02g47660 | Os.7751.1.S1_at | 2.25 | 2.24 | 1.9E-03 | 24.73 | 3.01 | 434 | 367 | 310 | -25 | none | + | - | Basic helix-loop-helix, putative, expressed |
Tal2c | 03g03034 | Os.10510.1.S1_at Os.53217.1.S1_x_at | 1.49 1.26 | 3.11 2.83 | 1.1E-02 6.8E-02 | 19.55 | 1.83 | 0 | 142 | 114 | -779 | 6 | - | + | Flavonol synthase/flavanone 3-hydroxylase, putative, expressed |
Tal3b | 03g03034 | Os.10510.1.S1_at Os.53217.1.S1_x_at | 1.49 1.26 | 3.11 2.83 | 1.1E-02 6.8E-02 | 16.73 | 2.76 | 258 | 759 | 567 | none | none | + | - | Flavonol synthase/flavanone 3-hydroxylase, putative, expressed |
Tal11a | 03g05370 | OsAffx.24978.1.S1_at | 10.98 | 13.02 | 5.2E-04 | 17.39 | 2.74 | 307 | 798 | 331 | 526 | none | + | - | Expressed protein |
Tal3c | 03g07540 | OsAffx.3165.1.S1_at | 6.33 | 3.84 | 3.6E-02 | 12.33 | 2.17 | 350 | 248 | 99 | -625 | none | - | + | bHLH family protein, putative, expressed |
Tal7 | 03g25490 | Os.34992.2.S1_at | 2.10 | 2.02 | 3.8E-05 | 16.32 | 2.01 | 494 | 199 | 30 | -363 | 9 | + | - | Cytochrome P450 72A1, putative, expressed |
Tal4a | 03g37840 | Os.20541.1.S1_at | 2.24 | 1.96 | 2.2E-04 | 15.58 | 1.52 | 0 | 362 | 151 | -3 | none | - | + | Potassium transporter, putative, expressed |
Tal2d | 04g49194 | Os.17316.1.S1_at | 22.42 | 10.49 | 3.9E-07 | 8.22 | 1.26 | 0 | 101 | 26 | -715 | none | - | + | Naringenin,2-oxoglutarate 3-dioxygenase, putative, expressed |
Tal3a | 05g12450 | OsAffx.26856.1.S1_at | 1.81 | 1.34 | 2.3E-01 | 16.07 | 2.01 | 294 | 446 | 315 | none | none | + | - | Hydroquinone glucosyltransferase, putative, expressed |
Tal3b | 05g27590 | Os.57186.1.S1_at | 2.40 | 4.42 | 3.4E-08 | 11.40 | 1.88 | 2 | 103 | 33 | -1 | none | - | + | Wound-induced protein WI12, putative, expressed |
Tal11b | 06g14750 | OsAffx.15432.1.S1_at | 1.29 | 1.30 | 2.0E-01 | 12.44 | 2.77 | 129 | 313 | 195 | 160 | -15 | + | - | Phosphatidylinositol-4-phosphate 5-Kinase family protein, putative, expressed |
Tal1c | 06g14750 | OsAffx.15432.1.S1_at | 1.29 | 1.30 | 2.0E-01 | 12.00 | 2.44 | 256 | 178 | 47 | none | none | + | - | Phosphatidylinositol-4-phosphate 5-Kinase family protein, putative, expressed |
Tal2a | 06g14750 | OsAffx.15432.1.S1_at | 1.29 | 1.30 | 2.0E-01 | 17.59 | 1.94 | 88 | 79 | -22 | -618 | -33 | nd | - | Phosphatidylinositol-4-phosphate 5-Kinase family protein, putative, expressed |
Tal4c | 06g37080 | Os.16282.1.A1_at OsAffx.15788.1.S1_at | 5.54 11.84 | 7.15 9.94 | 2.7E-10 6.3E-09 | 14.64 | 1.78 | 0 | 150 | 39 | -1 | none | - | + | L-ascorbate oxidase precursor, putative, expressed |
Tal8 | 06g37080 | Os.16282.1.A1_at OsAffx.15788.1.S1_at | 5.54 11.84 | 7.15 9.94 | 2.7E-10 6.3E-09 | 19.92 | 2.32 | 605 | 661 | 560 | -36 | 548 | + | - | L-ascorbate oxidase precursor, putative, expressed |
Tal2g | 06g46500 | Os.49496.1.S1_at | 6.40 | 6.88 | 4.3E-08 | 14.27 | 2.01 | 117 | 89 | 59 | -489 | -47 | - | + | Monocopper oxidase, putative, expressed |
Tal11a | 06g47950 | OsAffx.15977.1.S1_s_at | 1.78 | 1.67 | 2.8E-02 | 16.20 | 2.55 | 19 | 527 | none | -328 | 0 | nd | nd | Tetratricopeptide-like helical, putative, expressed |
Tal1c | 07g06970 | Os.49794.1.S1_at | 2.95 | 2.27 | 1.3E-02 | 5.97 | 1.22 | 0 | 216 | 24 | none | none | - | + | HEN1, putative, expressed |
Tal3a | 07g06970 | Os.49794.1.S1_at | 2.95 | 2.27 | 1.3E-02 | 16.21 | 2.03 | 354 | 930 | 815 | 444 | none | + | - | HEN1, putative, expressed |
Tal4b | 07g34510 | Os.51294.1.S1_at | 0.95 | 1.00 | 2.8E-01 | 8.88 | 1.63 | 33 | 302 | 151 | -425 | none | nd | nd | Retrotransposon protein, putative, unclassified, expressed |
Tal3b | 07g36430 | Os.31021.1.S1_at | 2.53 | 2.40 | 2.6E-02 | 15.78 | 2.6 | 108 | 117 | 31 | -4 | none | - | + | Expressed protein |
Tal6 | 07g47790 | Os.8920.1.S1_at | 4.16 | 8.41 | 3.6E-02 | 13.38 | 1.7 | 8 | 798 | 610 | -192 | 694 | + | - | AP2 domain containing protein, expressed |
Tal4a | 09g20220 | Os.4759.1.S1_at | 2.17 | 2.38 | 4.9E-02 | 28.93 | 2.83 | 280 | 170 | 139 | -751 | 34 | + | - | Glutathione S-transferase, putative, expressed |
Tal2d | 09g23560 | Os.5983.1.S1_at | 2.19 | 5.02 | 2.8E-01 | 14.19 | 2.17 | 288 | 525 | none | none | 93 | nd | nd | Dehydrogenase, putative, expressed |
Tal6 | 09g29100 | Os.18607.1.S1_at | 1.64 | 1.97 | 3.6E-02 | 17.00 | 2.13 | 167 | 0 | 0 | 0 | 0 | - | + | Cyclin, putative, expressed |
Tal4b | 09g32100 | Os.16365.1.S1_at | 3.34 | 2.45 | 8.0E-03 | 8.15 | 1.5 | 16 | 270 | 84 | 21 | none | - | + | Expressed protein |
Tal1b | 10g38489 | Os.2612.1.S1_at | 4.75 | 4.14 | 4.00E-07 | 8.75 | 4.13 | 325 | 64 | 20 | none | none | nt | nt | glutathione S-transferase GSTU6, putative, expressed |
Tal9a | 11g01480 | Os.18448.1.S1_s_at OsAffx.30765.1.S1_at | 5.42 5.74 | 3.94 4.10 | 8.2E-06 5.4E-06 | 19.71 | 2.56 | 206 | 776 | 621 | 365 | none | + | - | MYB family transcription factor, putative, expressed |
Tal9a | 12g01490 | Os.18448.1.S1_at | 5.21 | 3.92 | 2.6E-05 | 19.71 | 2.56 | 205 | 302 | 191 | 151 | none | + | - | MYB family transcription factor, putative, expressed |
Tal6 | 12g42970 | Os.11382.1.S1_at | 2.31 | 1.65 | 2.2E-04 | 16.84 | 2.14 | 139 | 132 | 30 | -565 | 12 | - | + | GATA zinc finger domain containing protein, expressed |
Tal6 | 12g42970 | Os.11382.1.S1_at | 2.31 | 1.65 | 2.2E-04 | 18.27 | 2.32 | 411 | 107 | 5 | -590 | -13 | - | + | GATA zinc finger domain containing protein, expressed |
Expression values are from the GeneChip expression experiment; see Materials and Methods.
Prefix “LOC_Os” is omitted.
Fold change in transcript abundance in leaves at 96h relative to 2h after inoculation with
Fold change in transcript abundance at 96h in Xoc-inoculated leaves relative to mock-inoculated leaves.
Calculated for the comparison of transcript abundance in Xoc vs. mock inoculated leaves across all time points.
Score is according to Doyle et al. [32] except that new RVDs ‘SN’ and ‘YG’, present in Tal2g, were assigned nucleotide association frequencies of ‘NN’ and ‘NG’, respectively (see text)
EBE relative score, ratio of the observed EBE score to the best possible score for the TAL effector [32].
EBE rank among the single best scoring sites for the TAL effector in each rice promoter [32].
Distance in bases from the 5' end of the EBE to the translational start site (TLS) of the target locus; a positive value indicates a location downstream of the EBE.
Distance in bases from the 5' end of the EBE to the transcriptional start site (TXS) based on cDNA evidence in the Rice Genome Annotation Project Release 7 (
Distance in bases from the 5' end of the EBE to the nearest identified putative TATA box; a positive value indicates a location downstream of the EBE; none, putative TATA box not present.
Distance in bases from the 5' end of the EBE to the nearest identified putative Y patch; a positive value indicates a location downstream of the EBE; none, putative Y patch not present.
Results of RT-PCR 48h after inoculation, relative to a negative control inoculation (see Supplemental Figure S1); Xoc,
The corrected
The corrected Table S7 can be downloaded here. The legend remains unchanged.
All computationally predicted targets in rice (cv. Nipponbare) of TAL effectors of
(XLSX)